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Although we have been talking about the microbiome for years, news about our microbial friends was huge this year.

We have known for some time that the microbes in our gut were extremely important for our health, but recently studies are beginning to show that the gut biome is even more important than we previously imagined.

Fecal Microbiota Transplantation, or FMTs, have been shown to cure Clostridium difficile infections in 90 percent of cases, a condition notoriously difficult to treat any other way. We don’t know exactly how FMTs work, other than that the introduction of microbiota (poop) from a healthy individual somehow causes the gut of an afflicted patient to regain its microbial diversity and rein in the rampant Clostridium difficile.

It appears that our gut microbes produce a wide variety of neurotransmitters that influence our brains, and vice versa, much more than previously believed. There is evidence that, in addition to mood, a number of brain disorders may be caused by microbial imbalance. The evidence is so strong that FMT banks such as OpenBiome have started screening donors for psychiatric problems in addition to a wide variety of health issues. Consequently, it is now harder to qualify as a donor to a fecal bank than it is to get into MIT or Harvard. Perhaps machines can help us here as they do everywhere else; Robogut is making headway in creating synthetic poop.

It has been shown that mice without gut microbes socialize less than mice with proper gut biomes, causing scientists to theorize that while socialization doesn’t help the fitness of mice, their social behavior and their habit of eating each other’s feces may be driven by the microbes “wanting” to be shared between the mice.

There is evidence that many of our favorite foods are really the favorite foods of our gut microbes, which turn those foods into things that our bodies need and like. Also, it appears that oligosaccharides which are abundant in breast milk and which are regarded to be metabolically "inert" to us selectively feed some of our “good” gut microbes. Not only are the microbes more abundant in the human body than human cells, it appears that they may be the reason we do many of the things that we do and are as important, if not more important, in many of the processes that occur in our body than our own cells.

However, not all microbes are good for us. In fact, most microbes are “neutral” and some are bad from the perspective of desirable health outcomes for us, the hosts. Take, for example, Toxoplasma gondii, which causes infected rats to lose their natural fear of cats because Toxoplasma gondii requires cats to reproduce sexually. Or rabies that causes animals to attack other animals to increase transmission. It could be more than just our mood that is controlled by microbes.

And the microbes are everywhere. The detergents that we use have eliminated the ammonia-oxidizing bacteria (AOB) on our skin—a bacterial that is present on the skin of all Yanomami, the indigenous people in the Amazon rainforest. It turns out that pre moser hygiene tribes like the Yanomami, among other things, do not suffer from acne or most forms of inflammatory skin diseases. In a study of over a thousand of members of the Kitavan Islanders of Papua New Guinea, there was not a single case. There is increasing evidence that allergies and many modern ailments have come into existence only after the invention of modern hygiene.

The microbes in the air are also part of the system. There are studies showing that infection rates in hospitals decrease if you open a window and let the diverse outdoor microbes in compared to aggressive systems that filter and sterilize the air.

The microbes in the soil appear to be an essential part of the system to produce the nutrients for our plants and the microbes in the plants are an essential part of how the plants convert the nutrients into flavors and nutrients for us. Generations of using artificial fertilizers, destroying the microbial flora of our soil and then later “enriching” our blank calories with the over-simplistic vitamins that happen to be the molecule de jour may have been exactly the opposite of what we should be doing.

The human gut, particularly the colon, has the highest recorded microbial density of any known microbial habitat. Our gut is almost the perfect environment to support the biodiversity and complexity that is our gut biome. The temperatures are well regulated, with us, the human host, able to survive in extreme conditions. The host can travel to extreme distances though their lifetime transporting and sharing microbes with these environments. From the perspective of the microbes, we are an almost perfectly evolved life support system for them. Maybe it’s arrogant to think about the microbes as some sort of “little helpers” in our system, but maybe it’s more accurate to think of us as architectural innovations by the microbes.

As we understand more and more about the genome, the epigenome, the brain, and the variety of complex systems that make us what we are, and the more I learn about the microbiome, the more it feels like maybe modern medicine is like the proverbial aliens trying to understand human motivation by only looking at the cars on the freeway through a telescope and that we have a long way to go before we will really understand what’s going on.